26a5ab042e
- use autosummary (with custom module template) - updated module docs for all modules so that they are included with sphinx autodocs
70 lines
2.3 KiB
Python
70 lines
2.3 KiB
Python
"""
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Script functionality
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====================
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The :mod:`run` module provides a high-level interface to PROPKA 3.
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The :program:`propka3` script consists of the :func:`main`
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function. If similar functionality is desired from a Python script
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(without having to call the :program:`propka` script itself) then the
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:func:`single` function can be used instead.
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"""
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import logging
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from propka.lib import loadOptions
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from propka.input import read_parameter_file, read_molecule_file
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from propka.parameters import Parameters
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from propka.molecular_container import MolecularContainer
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_LOGGER = logging.getLogger("PROPKA")
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def main(optargs=None):
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"""Read in structure files, calculate pKa values, and print pKa files."""
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# loading options, flags and arguments
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optargs = optargs if optargs is not None else []
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options = loadOptions(*optargs)
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pdbfiles = options.filenames
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parameters = read_parameter_file(options.parameters, Parameters())
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for pdbfile in pdbfiles:
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my_molecule = MolecularContainer(parameters, options)
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my_molecule = read_molecule_file(pdbfile, my_molecule)
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my_molecule.calculate_pka()
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my_molecule.write_pka()
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if options.generate_propka_input:
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my_molecule.write_propka()
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def single(pdbfile, optargs=None):
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"""Run a single PROPKA calculation using *pdbfile* as input.
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Commandline options can be passed as a **list** in *optargs*.
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Example
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-------
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Given an input file "protein.pdb", run the equivalent of ``propka3
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--mutation=N25R/N181D -v --pH=7.2 protein.pdb`` as::
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propka.run.single("protein.pdb",
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optargs=["--mutation=N25R/N181D", "-v", "--pH=7.2"])
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.. todo::
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Test :func:`single`, not sure if it is correctly processing ``pdbfile``.
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"""
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optargs = optargs if optargs is not None else []
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options = loadOptions(*optargs)
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pdbfile = options.filenames.pop(0)
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parameters = read_parameter_file(options.parameters, Parameters())
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if len(options.filenames) > 0:
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_LOGGER.warning("Ignoring filenames: {0:s}".format(options.filenames))
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my_molecule = MolecularContainer(parameters, options)
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my_molecule = read_molecule_file(pdbfile, my_molecule)
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my_molecule.calculate_pka()
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my_molecule.write_pka()
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if options.generate_propka_input:
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my_molecule.write_propka()
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return my_molecule
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